Therapeutic targeting of a microRNA to treat Duchenne muscular dystrophy

ABSTRACT

Methods of treating Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD), comprising administering an inhibitory nucleic acid that targets miR-128.

CLAIM OF PRIORITY

This application is a continuation of U.S. patent application Ser. No.16/345,635, filed Apr. 26, 2019, which is a § 371 National StageApplication of PCT/US2017/052047, filed Sep. 18, 2017, which claims thebenefit of U.S. Provisional Application Ser. No. 62/413,469, filed onOct. 27, 2016; and 62/523,923, filed on Jun. 23, 2017. The entirecontents of the foregoing are incorporated herein by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Mar. 19, 2020, isnamed Sequence Listing_SL.txt, and 3,797 bytes in size.

TECHNICAL FIELD

Described herein are methods of treating Duchenne muscular dystrophy(DMD) and Becker muscular dystrophy (BMD), comprising administering aninhibitory nucleic acid that targets miR-128.

BACKGROUND

Duchenne muscular dystrophy (DMD), an X-linked inherited neuromusculardisorder, has a worldwide incidence of one in ˜3,500 live male births,making it the most common muscular dystrophy. It is caused by mutationsin the dystrophin gene, resulting in the progressive loss of skeletaland cardiac muscle. It is an early lethal disease, and most afflictedmales die in their 20's or 30's due to cardiac or respiratorycomplications. In addition to steroids, which are able to modestly slowdisease progression, an exon-skipping therapy was recently approved forthe treatment of DMD. However, it only partly improves the symptoms of13% of patients. There is thus an urgent need for novel therapeuticavenues for the treatment of DMD.

SUMMARY

The present invention is based, at least in part, on the discovery thatmiR-128-1 is a key regulator of mitochondrial metabolism in skeletalmuscle cells and tissues through modulation of the expression of anumber of proteins implicated in DMD, such as PGC-1α, SIRT1, AMPKα2,CPT1β and PPARα. miR-128-1 is also predicted to target JAG1, as well asthe autophagy factor ULK1, and WNT7A, whose over-expression alsoimproves DMD phenotypes in mdx mice. Potent positive effects wereobserved after miR-128-1 locked nucleic acid (LNA) antisenseoligonucleotide (ASO) treatment on the energy expenditure program inmurine C2C12 myotubes, and increased numbers of mitochondria andelevated energy expenditure gene expression (e.g., PGC-1α, SIRT1,AMPKα2, PPARα, and UCP3) were seen in skeletal muscle in mice. Inaddition, as shown herein, LNA ASOs targeting miR-128-1 in zebrafish(fish miR-128-1 is identical to mouse and human) strongly amelioratedskeletal muscle-related phenotypes in the sapje-likedystrophin-deficient zebrafish model, resulting in a marked decrease inskeletal muscle abnormalities and rescue of swim velocity/distance tonear wild-type levels. Finally, injection of anti-miR-128-1 LNA ASOs inmdx mice decreased pathological muscle phenotypes in this model. ThusmiR-128-1 is a target for highly potent and specific LNA ASOtherapeutics for the treatment of DMD.

This provided herein are methods for treating a subject who has Duchennemuscular dystrophy (DMD) or Becker muscular dystrophy (BMD). The methodsinclude administering to the subject a therapeutically effective amountof an inhibitory nucleic acid that is complementary to all or part ofany of SEQ ID NOs: 1-6.

Also provided herein are methods for increasing muscle mass, or reducingor delaying muscle loss, e.g., in a subject who has Duchenne musculardystrophy (DMD) or Becker muscular dystrophy (BMD). The methods includeadministering to the subject a therapeutically effective amount of aninhibitory nucleic acid that is complementary to all or part of any ofSEQ ID NOs:1-6.

Further, provided herein are methods for treating, or reducing risk ofdeveloping, dilated cardiomyopathy (DCM) in a subject, e.g., wherein thesubject has Duchenne muscular dystrophy (DMD) or Becker musculardystrophy (BMD). The methods include administering to the subject aninhibitory nucleic acid sequence that is complementary to all or part ofany of SEQ ID NOs:1-6.

In some embodiments, the inhibitory nucleic acid is complementary to allor part of SEQ ID NO:2.

In some embodiments, the inhibitory nucleic acid is complementary to atleast nucleotides 2-7 (5′-CACAGU-3′) of SEQ ID NO:3.

In some embodiments, the inhibitory nucleic acid is an antisenseoligonucleotide.

In some embodiments, the antisense oligonucleotide comprises a sequencethat complementary to SEQ ID NO:3.

In some embodiments, the inhibitory nucleic acid is an interfering RNA.

In some embodiments, the interfering RNA is a small hairpin RNA (shRNA)or small interfering RNA (siRNA).

In some embodiments, the inhibitory nucleic acid sequence inhibitspost-transcriptional processing of SEQ ID NO:1 or 5.

In some embodiments, the subject has DMD or BMD.

In some embodiments, the methods include selecting a subject on thebasis that they have DMD or BMD.

In some embodiments, the inhibitory nucleic acid has at least one lockednucleotide.

In some embodiments, the inhibitory nucleic acid has a phosphorothioatebackbone.

In some embodiments, the inhibitory nucleic acid is or comprisesTTCACTGTG (SEQ ID NO:10) or GGTTCACTGTG (SEQ ID NO:11),

In some embodiments, at least half of the nucleic acids are locked

In some embodiments, all of the nucleic acids are locked.

In some embodiments, the backbone is a phosphorothioate backbone.

In some embodiments, the inhibitory nucleic acid is or comprises+G*+G*+T*+T*C*A*C*+T*+G*+T*+G (SEQ ID NO:8).

In some embodiments, the inhibitory nucleic acid is administered at adose of 1-20 mg/kg.

In some embodiments, the inhibitory nucleic acid is administered once ortwice per month.

Also provided herein are inhibitory nucleic acids that are or comprise+G*+G*+T*+T*C*A*C*+T*+G*+T*+G (SEQ ID NO:8), as well as pharmaceuticalcompositions comprising the inhibitory nucleic acids described herein.

In addition, provided herein are inhibitory nucleic acids that arecomplementary to all or part of any of SEQ ID NOs: 1-6 for use in amethod of treating a subject who has Duchenne muscular dystrophy (DMD)or Becker muscular dystrophy (BMD); for use in a method of increasingmuscle mass, or reducing or delaying muscle loss, in a subject who hasDuchenne muscular dystrophy (DMD) or Becker muscular dystrophy (BMD); orfor use in a method of treating, or reducing risk of developing, dilatedcardiomyopathy (DCM) in a subject who has Duchenne muscular dystrophy(DMD) or Becker muscular dystrophy (BMD). In some embodiments, theinhibitory nucleic acid is or comprises +G*+G*+T*+T*C*A*C*+T*+G*+T*+G(SEQ ID NO:8).

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Methods and materials aredescribed herein for use in the present invention; other, suitablemethods and materials known in the art can also be used. The materials,methods, and examples are illustrative only and not intended to belimiting. All publications, patent applications, patents, sequences,database entries, and other references mentioned herein are incorporatedby reference in their entirety. In case of conflict, the presentspecification, including definitions, will control.

Other features and advantages of the invention will be apparent from thefollowing detailed description and figures, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1 shows the sequence of human miR-128-1 precursor, also known asmiR-128A precursor (SEQ ID NO:1).

FIG. 2 shows the sequence of mature human miR-128 DNA (SEQ ID NO:2) andRNA (SEQ ID NO:3). The mature sequences are the same for miR-128-1 andmiR-128-2.

FIG. 3 shows the predicted hairpin structure of miR-128-1 precursor RNA(SEQ ID NO:4).

FIG. 4 shows the sequence of human miR-128-2 precursor, also known asmiR-128B precursor (SEQ ID NO:5).

FIG. 5 shows the predicted hairpin structure of miR-128-2 precursor RNA(SEQ ID NO:6).

FIGS. 6A-C. AntimiR-128-1 treatment of diet-induced obese (DIO) miceresults in elevated expression of genes involved in mitochondrialbiogenesis and energy expenditure (6A, 6B), and increased numbers ofmitochondria (6C) in skeletal muscle.

FIGS. 7A-C. Anti-miR-128-1 treatment of C2C12 myotubes results inknock-down of miR-128-1 (7A) and elevated expression of genes involvedin mitochondrial biogenesis and energy expenditure (7B, 7C), a number ofwhich have been implicated as modifiers downstream of dystrophin loss inDMD.

FIGS. 8A-F. Anti-miR-128-1 treatment of C2C12 cells results in increasedpotency of the AMPK activator AICAR and in increased mitochondrialenergy expenditure. 8A-D. Increased AICAR-stimulated expression ofAMPKa2, PGC-1α, PPARα, and CPT1β in response to anti-miR-128-1 treatmentof C2C12 myoblasts. 8E. Elevated mitochondrial respiration in C2C12cells after anti-miR-128-1 treatment, as determined by Seahorseanalysis. 8F. Increased fatty acid β-oxidation in C2C12 cells inresponse to anti-miR-128-1 treatment.

FIGS. 9A-C 9mer-LNA inhibiting miR128 restored sapje-like fish musclephenotype. 9A. Representative picture of affected fish birefringence.9B. 9mer consistently reduced the ratio of affected fish in progeny. 9C.Sequencing confirmed the restoring of muscle structure after 9mer LNAtreatment.

FIGS. 10A-B. Anti-miR128 9mer LNA significantly improved dystrophin−/−sapje-like fish activity. 9mer LNA significantly increased the velocity(10A) and the total distance (10B) of dystrophin−/− fish at 5 dpf to alevel comparable to wildtype fish.

FIGS. 11A-C. Pilot study of LNA ASO treatment targeting miR-128-1 in themdx mouse DMD model. 11A. Decreased miR-128-1 levels in TA muscle inresponse to anti-miR-128-1 LNA ASO treatment. 11B. Lowered circulatingcreatine kinase in anti-miR-128-1-treated mdx mice. 11C. Treatment withanti-miR-128-1 LNA ASOs resulted in increased grip strength in thetwo-limb hanging grip test.

DETAILED DESCRIPTION

Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD)are inherited progressive muscle disorders that are non-inflammatory andnot associated with a central or peripheral nerve abnormality. Thedisease affects the muscles with definite fiber degeneration but withoutevidence of morphologic aberrations, resulting in progressive musclewasting, and are caused by defects in the dystrophin gene DMD. See,e.g., Aartsma-Rus et al., J Med Genet. 2016 March; 53(3):145-51;Flanigan et al., Hum Mutat. 2011 March; 32(3): 299-308. In some cases,DMD or BMD are caused by mutations that affect splicing of thetranscript, e.g., acceptor or donor splice site mutations.

Dilated cardiomyopathy (DCM) is a progressive disease of the cardiacmuscle characterized by ventricular chamber enlargement and contractiledysfunction (See, e.g., Nguyen et al., Dilated Cardiomyopathy, 2017,available at emedicine.medscape.com/article/152696-overview; Richardsonet al., Circulation. 1996; 93(5):841; Elliott, Heart. 2000; 84(1):106;Luk et al., J Clin Pathol. 2009; 62(3):219. DCM is a late manifestationin DMD, with >90% of older boys showing symptoms, and a leading cause ofheart failure and death (see, e.g., Kamdar and Garry, J. Amer. Coll.Cardiol. 2016 May 31(67): 2533-46). Recent findings have suggested thatdown-regulation of PPARalpha and PGClalpha/beta in cardiac muscle in DCMleads to decreased mitochondrial function and oxidative stress thatsignificantly contributes to the DCM pathologies (e.g., Burke et al. JCIInsight 2016; 1(6):e86898; Chang et al. PNAS 2016 Nov. 15(113):13120-25).

A number of therapeutic strategies for DMD/BMD are currently beingpursued, including approaches that attempt to ameliorate the splicingerrors or target the secondary deleterious effects downstream ofdystrophin deficiency, such as abnormal mitochondrial metabolism andautophagy.

Glucocorticoid treatment remains the standard of care for DMD, butexhibits limited efficacy and long-term use is associated with moderateto serious side effects such as immune suppression, weight gain, boneloss and abnormal glucose regulation¹. A number of new approaches to thetreatment of DMD are being pursued¹, including strategies to restoredystrophin such as exon-skipping antisense oligonucleotide (ASO)therapies, CRSPR-Cas9-based corrective mutagenesis, and virus-baseddystrophin replacement. Although much excitement greeted the recent FDAapproval of an exon-skipping therapy for DMD produced by SareptaTherapeutics, this treatment only modestly improves ambulation as itgenerates a truncated and partially functional dystrophin protein akinto that found in the milder Becker-type of muscular dystrophy².Moreover, it is limited to the ˜13% of patients that have mutationswhere skipping exon 51 will restore the dystrophin translational readingframe and produce protein. The lack of efficacious treatments for mostDMD patients highlights an urgent need for novel therapeuticinterventions for this devastating disease.

miRNAs are short (˜18-24 nucleotide) non-coding RNAs with diversefunctions in development, metabolism and disease⁵³. They regulate geneexpression by base-pairing with partially complementary sequencesprimarily located in the 3′UTRs of target mRNAs and thereby promote mRNAdegradation or translational repression⁵⁴⁻⁵⁷. Each miRNA has thepotential to target a large number of mRNAs as predicted bycomplementarity to the miRNA seed region and non-seed sequences⁵⁵, andfrequently control multiple genes in linked pathways, thereby exerting alarger cumulative effect. Owing to their short but highly specificsequence recognition motifs and, not uncommonly, marked regulatoryimpact on pathways important in physiology and disease, miRNAs representattractive targets of potent and highly sequence-selective antisenseoligonucleotides (ASOs).

As shown herein, miR-128-1 directly targets PPARalpha and PGC1alpha inskeletal muscle, accompanied by down-regulation of mitochondrialbiogenesis and function (see the Examples), with LNA ASO treatmentameliorating these defects in DMD. In addition, as the heart is also astriated muscle, it is believed that miR-128-1 plays a pathological rolein DCM in general, but in particular in the context of DMD.

Methods of Treatment

The methods described herein include the inhibition of miR-128 in asubject who has DMD or BMD, and/or has DCM, to thereby treat thesubject. For example, the methods can achieve a therapeutic effect,e.g., reduction in muscle weakness or a reduction in rate of muscle lossor weakening; increasing muscle mass; reducing or delaying muscle loss;or treating, or reducing risk of developing, DCM, e.g., in a subject whohas DMD or BMD. This can be achieved, for example, by administering aninhibitory nucleic acid, e.g., an antisense oligonucleotide that iscomplementary to miR-128, including but not limited to an antisenseoligonucleotide comprising all or part of AAAGAGACCGGTTCACTGTGA (SEQ IDNO:7); in some embodiments, as described in further detail below, theoligo includes different modifications, e.g., in the sugar backbone, tomake it more cell permeable and nuclease resistant on one hand, andphysiologically non-toxic at low concentrations on the other.

In some embodiments, the oligo is an LNA comprising the sequence

-   -   +G*+G*+T*+T*C*A*C*+T*+G*+T*+G (SEQ ID NO:8)    -   * indicates PS link    -   + indicates LNA modification        Other inhibitory nucleic acids for use in practicing the methods        described herein and that are complementary to miR-128 can be        those that inhibit post-transcriptional processing of miR-128,        such as an interfering RNA, including but not limited to an        shRNA or siRNA, or an antagomir.

Inhibitory Nucleic Acids

Inhibitory nucleic acids useful in the present methods and compositionsinclude antisense oligonucleotides, modified bases/locked nucleic acids(LNAs), antagomirs, peptide nucleic acids (PNAs), and other oligomericcompounds or oligonucleotide mimetics which hybridize to at least aportion of the target nucleic acid (i.e., miR-128, e.g., all or part ofany of SEQ ID NOs:1-6) and modulate its function; see, e.g., U.S. Pat.Nos. 9,045,749 and 9,476,046. In some embodiments, the inhibitorynucleic acids include antisense RNA, antisense DNA, chimeric antisenseoligonucleotides, antisense oligonucleotides comprising modifiedlinkages, or combinations thereof. See, e.g., WO 2010040112.

In some embodiments, the inhibitory nucleic acids are 9 to 50, 9 to 21,13 to 50, or 13 to 30 nucleotides in length. One having ordinary skillin the art will appreciate that this embodies oligonucleotides havingantisense portions of 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides in length, orany range therewithin. In some embodiments, the oligonucleotides are 15nucleotides in length. In some embodiments, the antisense oroligonucleotide compounds of the invention are 12 or 13 to 30nucleotides in length. One having ordinary skill in the art willappreciate that this embodies inhibitory nucleic acids having antisenseportions of 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29 or 30 nucleotides in length, or any range therewithin.

In some embodiments, the inhibitory nucleic acids are designed to targeta specific region of miR-128. For example, a specific functional regioncan be targeted, e.g., a region comprising a seed sequence or a regioncomplementary to the target nucleic acid on which the miR-128 acts. Forexample, the inhibitory nucleic acid can be designed to target at leastnucleotides 2-10 of the mature miR-128-1, e.g., complementary toCACAGUGAA (SEQ ID NO:9), e.g., have the sequence TTCACTGTG (SEQ IDNO:10, which is the same as nucleotides 12-20 of SEQ ID NO:7).Alternatively or in addition, highly conserved regions can be targeted,e.g., regions identified by aligning sequences from disparate speciessuch as primate (e.g., human) and rodent (e.g., mouse) and looking forregions with high degrees of identity. Percent identity can bedetermined routinely using basic local alignment search tools (BLASTprograms) (Altschul et al., J. Mol. Biol., 1990, 215, 403-410; Zhang andMadden, Genome Res., 1997, 7, 649-656), e.g., using the defaultparameters.

In some embodiments, the inhibitory nucleic acids are chimericoligonucleotides that contain two or more chemically distinct regions,each made up of at least one nucleotide. These oligonucleotidestypically contain at least one region of modified nucleotides thatconfers one or more beneficial properties (such as, for example,increased nuclease resistance, increased uptake into cells, increasedbinding affinity for the target) and a region that is a substrate forenzymes capable of cleaving RNA:DNA or RNA:RNA hybrids. Chimericinhibitory nucleic acids of the invention may be formed as compositestructures of two or more oligonucleotides, modified oligonucleotides,oligonucleosides and/or oligonucleotide mimetics as described above.Such compounds have also been referred to in the art as hybrids orgapmers. In some embodiments, the oligonucleotide is a gapmer (contain acentral stretch (gap) of DNA monomers sufficiently long to induce RNaseH cleavage, flanked by blocks of LNA modified nucleotides; see, e.g.,Stanton et al., Nucleic Acid Ther. 2012. 22: 344-359; Nowotny et al.,Cell, 121:1005-1016, 2005; Kurreck, European Journal of Biochemistry270:1628-1644, 2003; Fluiter et al., Mol Biosyst. 5(8):838-43, 2009). Insome embodiments, the oligonucleotide is a mixmer (includes alternatingshort stretches of LNA and DNA; Naguibneva et al., Biomed Pharmacother.2006 November; 60(9):633-8; from et al., Gene. 2006 May 10;3720:137-41). Representative United States patents that teach thepreparation of such hybrid structures comprise, but are not limited to,U.S. Pat. Nos. 5,013,830; 5,149,797; 5,220,007; 5,256,775; 5,366,878;5,403,711; 5,491,133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; and5,700,922, each of which is herein incorporated by reference.

In some embodiments, the inhibitory nucleic acid comprises at least onenucleotide modified at the 2′ position of the sugar, most preferably a2′-O-alkyl, 2′-O-alkyl-O-alkyl or 2′-fluoro-modified nucleotide. Inother preferred embodiments, RNA modifications include 2′-fluoro,2′-amino and 2′ O-methyl modifications on the ribose of pyrimidines,abasic residues or an inverted base at the 3′ end of the RNA. Suchmodifications are routinely incorporated into oligonucleotides and theseoligonucleotides have been shown to have a higher Tm (i.e., highertarget binding affinity) than; 2′-deoxyoligonucleotides against a giventarget.

A number of nucleotide and nucleoside modifications have been shown tomake the oligonucleotide into which they are incorporated more resistantto nuclease digestion than the native oligodeoxynucleotide; thesemodified oligos survive intact for a longer time than unmodifiedoligonucleotides. Specific examples of modified oligonucleotides includethose comprising modified backbones, for example, phosphorothioates,phosphotriesters, methyl phosphonates, short chain alkyl or cycloalkylintersugar linkages or short chain heteroatomic or heterocyclicintersugar linkages. Most preferred are oligonucleotides withphosphorothioate backbones and those with heteroatom backbones,particularly CH₂—NH—O—CH₂, CH, ˜N(CH₃)˜O˜CH₂ (known as amethylene(methylimino) or MMI backbone], CH₂—O—N(CH₃)—CH₂,CH₂—N(CH₃)—N(CH₃)—CH₂ and O—N(CH₃)—CH₂—CH₂ backbones, wherein the nativephosphodiester backbone is represented as O—P—O—CH); amide backbones(see De Mesmaeker et al. Ace. Chem. Res. 1995, 28:366-374); morpholinobackbone structures (see Summerton and Weller, U.S. Pat. No. 5,034,506);peptide nucleic acid (PNA) backbone (wherein the phosphodiester backboneof the oligonucleotide is replaced with a polyamide backbone, thenucleotides being bound directly or indirectly to the aza nitrogen atomsof the polyamide backbone, see Nielsen et al., Science 1991, 254, 1497).Phosphorus-containing linkages include, but are not limited to,phosphorothioates, chiral phosphorothioates, phosphorodithioates,phosphotriesters, aminoalkylphosphotriesters, methyl and other alkylphosphonates comprising 3′alkylene phosphonates and chiral phosphonates,phosphinates, phosphoramidates comprising 3′-amino phosphoramidate andaminoalkylphosphoramidates, thionophosphoramidates,thionoalkylphosphonates, thionoalkylphosphotriesters, andboranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs ofthese, and those having inverted polarity wherein the adjacent pairs ofnucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′; see U.S.Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196;5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131;5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925;5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799;5,587,361; and 5,625,050.

Morpholino-based oligomeric compounds are described in Dwaine A. Braaschand David R. Corey, Biochemistry, 2002, 41(14), 4503-4510); Genesis,volume 30, issue 3, 2001; Heasman, J., Dev. Biol., 2002, 243, 209-214;Nasevicius et al., Nat. Genet., 2000, 26, 216-220; Lacerra et al., Proc.Natl. Acad. Sci., 2000, 97, 9591-9596; and U.S. Pat. No. 5,034,506,issued Jul. 23, 1991.

Cyclohexenyl nucleic acid oligonucleotide mimetics are described in Wanget al., J. Am. Chem. Soc., 2000, 122, 8595-8602.

Modified oligonucleotide backbones that do not include a phosphorus atomtherein have backbones that are formed by short chain alkyl orcycloalkyl internucleoside linkages, mixed heteroatom and alkyl orcycloalkyl internucleoside linkages, or one or more short chainheteroatomic or heterocyclic internucleoside linkages. These comprisethose having morpholino linkages (formed in part from the sugar portionof a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfonebackbones; formacetyl and thioformacetyl backbones; methylene formacetyland thioformacetyl backbones; alkene containing backbones; sulfamatebackbones; methyleneimino and methylenehydrazino backbones; sulfonateand sulfonamide backbones; amide backbones; and others having mixed N,O, S and CH2 component parts; see U.S. Pat. Nos. 5,034,506; 5,166,315;5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564;5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307;5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046;5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and5,677,439, each of which is herein incorporated by reference.

One or more substituted sugar moieties can also be included, e.g., oneof the following at the 2′ position: OH, SH, SCH₃, F, OCN, OCH₃ OCH₃,OCH₃O(CH₂)n CH₃, O(CH₂)n NH₂ or O(CH₂)n CH₃ where n is from 1 to about10; Ci to C10 lower alkyl, alkoxyalkoxy, substituted lower alkyl,alkaryl or aralkyl; Cl; Br; CN; CF3; OCF3; O-, S-, or N-alkyl; O-, S-,or N-alkenyl; SOCH3; SO2 CH3; ONO2; NO2; N3; NH2; heterocycloalkyl;heterocycloalkaryl; aminoalkylamino; polyalkylamino; substituted silyl;an RNA cleaving group; a reporter group; an intercalator; a group forimproving the pharmacokinetic properties of an oligonucleotide; or agroup for improving the pharmacodynamic properties of an oligonucleotideand other substituents having similar properties. A preferredmodification includes 2′-methoxyethoxy [2′-0-CH₂CH₂OCH₃, also known as2′-O-(2-methoxyethyl)] (Martin et al, HeIv. Chim. Acta, 1995, 78, 486).Other preferred modifications include 2′-methoxy (2′-0-CH₃), 2′-propoxy(2′-OCH₂ CH₂CH₃) and 2′-fluoro (2′-F). Similar modifications may also bemade at other positions on the oligonucleotide, particularly the 3′position of the sugar on the 3′ terminal nucleotide and the 5′ positionof 5′ terminal nucleotide. Oligonucleotides may also have sugar mimeticssuch as cyclobutyls in place of the pentofuranosyl group.

Inhibitory nucleic acids can also include, additionally oralternatively, nucleobase (often referred to in the art simply as“base”) modifications or substitutions. As used herein, “unmodified” or“natural” nucleobases include adenine (A), guanine (G), thymine (T),cytosine (C) and uracil (U). Modified nucleobases include nucleobasesfound only infrequently or transiently in natural nucleic acids, e.g.,hypoxanthine, 6-methyladenine, 5-Me pyrimidines, particularly5-methylcytosine (also referred to as 5-methyl-2′ deoxycytosine andoften referred to in the art as 5-Me-C), 5-hydroxymethylcytosine (HMC),glycosyl HMC and gentobiosyl HMC, as well as synthetic nucleobases,e.g., 2-aminoadenine, 2-(methylamino)adenine,2-(imidazolylalkyl)adenine, 2-(aminoalklyamino)adenine or otherheterosubstituted alkyladenines, 2-thiouracil, 2-thiothymine,5-bromouracil, 5-hydroxymethyluracil, 8-azaguanine, 7-deazaguanine, N6(6-aminohexyl)adenine and 2,6-diaminopurine. Kornberg, A., DNAReplication, W. H. Freeman & Co., San Francisco, 1980, pp 75-77;Gebeyehu, G., et al. Nucl. Acids Res. 1987, 15:4513). A “universal” baseknown in the art, e.g., inosine, can also be included. 5-Me-Csubstitutions have been shown to increase nucleic acid duplex stabilityby 0.6-1.2<0>C. (Sanghvi, Y. S., in Crooke, S. T. and Lebleu, B., eds.,Antisense Research and Applications, CRC Press, Boca Raton, 1993, pp.276-278) and are presently preferred base substitutions.

It is not necessary for all positions in a given oligonucleotide to beuniformly modified, and in fact more than one of the aforementionedmodifications may be incorporated in a single oligonucleotide or even atwithin a single nucleoside within an oligonucleotide.

In some embodiments, both a sugar and an internucleoside linkage, i.e.,the backbone, of the nucleotide units are replaced with novel groups.The base units are maintained for hybridization with an appropriatenucleic acid target compound. One such oligomeric compound, anoligonucleotide mimetic that has been shown to have excellenthybridization properties, is referred to as a peptide nucleic acid(PNA). In PNA compounds, the sugar-backbone of an oligonucleotide isreplaced with an amide containing backbone, for example, anaminoethylglycine backbone. The nucleobases are retained and are bounddirectly or indirectly to aza nitrogen atoms of the amide portion of thebackbone. Representative United States patents that teach thepreparation of PNA compounds comprise, but are not limited to, U.S. Pat.Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is hereinincorporated by reference. Further teaching of PNA compounds can befound in Nielsen et al, Science, 1991, 254, 1497-1500.

Inhibitory nucleic acids can also include one or more nucleobase (oftenreferred to in the art simply as “base”) modifications or substitutions.As used herein, “unmodified” or “natural” nucleobases comprise thepurine bases adenine (A) and guanine (G), and the pyrimidine basesthymine (T), cytosine (C) and uracil (U). Modified nucleobases compriseother synthetic and natural nucleobases such as 5-methylcytosine(5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine,2-aminoadenine, 6-methyl and other alkyl derivatives of adenine andguanine, 2-propyl and other alkyl derivatives of adenine and guanine,2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil andcytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine andthymine, 5-uracil (pseudo-uracil), 4-thiouracil, 8-halo, 8-amino,8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines andguanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other5-substituted uracils and cytosines, 7-methylquanine and7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and7-deazaadenine and 3-deazaguanine and 3-deazaadenine.

Further, nucleobases comprise those disclosed in U.S. Pat. No.3,687,808, those disclosed in ‘The Concise Encyclopedia of PolymerScience And Engineering’, pages 858-859, Kroschwitz, J. I., ed. JohnWiley & Sons, 1990, those disclosed by Englisch et al., AngewandleChemie, International Edition’, 1991, 30, page 613, and those disclosedby Sanghvi, Y. S., Chapter 15, Antisense Research and Applications',pages 289-302, Crooke, S. T. and Lebleu, B. ea., CRC Press, 1993.Certain of these nucleobases are particularly useful for increasing thebinding affinity of the oligomeric compounds of the invention. Theseinclude 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6substituted purines, comprising 2-aminopropyladenine, 5-propynyluraciland 5-propynylcytosine. 5-methylcytosine substitutions have been shownto increase nucleic acid duplex stability by 0.6-1.2<0>C (Sanghvi, Y.S., Crooke, S. T. and Lebleu, B., eds, ‘Antisense Research andApplications’, CRC Press, Boca Raton, 1993, pp. 276-278) and arepresently preferred base substitutions, even more particularly whencombined with 2′-O-methoxyethyl sugar modifications. Modifiednucleobases are described in 3,687,808, as well as U.S. Pat. Nos.4,845,205; 5,130,302; 5,134,066; 5,175,273; 5, 367,066; 5,432,272;5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540;5,587,469; 5,596,091; 5,614,617; 5,750,692, and 5,681,941, each of whichis herein incorporated by reference.

In some embodiments, the inhibitory nucleic acids are chemically linkedto one or more moieties or conjugates that enhance the activity,cellular distribution, or cellular uptake of the oligonucleotide. Suchmoieties comprise but are not limited to, lipid moieties such as acholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989,86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Let.,1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharanet al, Ann. N. Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al.,Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol(Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphaticchain, e.g., dodecandiol or undecyl residues (Kabanov et al., FEBSLett., 1990, 259, 327-330; Svinarchuk et al., Biochimie, 1993, 75,49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol ortriethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate(Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al.,Nucl. Acids Res., 1990, 18, 3777-3783), a polyamine or a polyethyleneglycol chain (Mancharan et al., Nucleosides & Nucleotides, 1995, 14,969-973), or adamantane acetic acid (Manoharan et al., TetrahedronLett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et al., Biochim.Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine orhexylamino-carbonyl-t oxycholesterol moiety (Crooke et al., J.Pharmacol. Exp. Ther., 1996, 277, 923-937). See also U.S. Pat. Nos.4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730;5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124;5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718;5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737;4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830;5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022;5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098;5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667;5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371;5,595,726; 5,597,696; 5,599,923; 5,599, 928 and 5,688,941, each of whichis herein incorporated by reference.

These moieties or conjugates can include conjugate groups covalentlybound to functional groups such as primary or secondary hydroxyl groups.Conjugate groups of the invention include intercalators, reportermolecules, polyamines, polyamides, polyethylene glycols, polyethers,groups that enhance the pharmacodynamic properties of oligomers, andgroups that enhance the pharmacokinetic properties of oligomers. Typicalconjugate groups include cholesterols, lipids, phospholipids, biotin,phenazine, folate, phenanthridine, anthraquinone, acridine,fluoresceins, rhodamines, coumarins, and dyes. Groups that enhance thepharmacodynamic properties, in the context of this invention, includegroups that improve uptake, enhance resistance to degradation, and/orstrengthen sequence-specific hybridization with the target nucleic acid.Groups that enhance the pharmacokinetic properties, in the context ofthis invention, include groups that improve uptake, distribution,metabolism or excretion of the compounds of the present invention.Representative conjugate groups are disclosed in International PatentApplication No. PCT/US92/09196, filed Oct. 23, 1992, and U.S. Pat. No.6,287,860, which are incorporated herein by reference. Conjugatemoieties include, but are not limited to, lipid moieties such as acholesterol moiety, cholic acid, a thioether, e.g., hexyl-5-tritylthiol,a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecylresidues, a phospholipid, e.g., di-hexadecyl-rac-glycerol ortriethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, apolyamine or a polyethylene glycol chain, or adamantane acetic acid, apalmityl moiety, or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety. See, e.g., U.S. Pat. Nos. 4,828,979; 4,948,882;5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717,5,580,731; 5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045;5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044;4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941; 4,835,263;4,876,335; 4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136;5,082,830; 5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506;5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723;5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552;5,567,810; 5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696;5,599,923; 5,599,928 and 5,688,941.

The inhibitory nucleic acids useful in the present methods aresufficiently complementary to all or part of miR-128, i.e., hybridizesufficiently well and with sufficient specificity, to give the desiredeffect. “Complementary” refers to the capacity for pairing, throughhydrogen bonding, between two sequences comprising naturally ornon-naturally occurring bases or analogs thereof. For example, if a baseat one position of an inhibitory nucleic acid is capable of hydrogenbonding with a base at the corresponding position of a miR-128 sequence,then the bases are considered to be complementary to each other at thatposition. 100% complementarity is not required.

In the context of this invention, hybridization means hydrogen bonding,which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogenbonding, between complementary nucleoside or nucleotide bases. Forexample, adenine and thymine are complementary nucleobases which pairthrough the formation of hydrogen bonds. Complementary, as used herein,refers to the capacity for precise pairing between two nucleotides. Theinhibitory nucleic acids and the miR-128 are complementary to each otherwhen a sufficient number of corresponding positions in each molecule areoccupied by nucleotides that can hydrogen bond with each other. Thus,“specifically hybridizable” and “complementary” are terms which are usedto indicate a sufficient degree of complementarity or precise pairingsuch that stable and specific binding occurs between the inhibitorynucleic acid and the miR-128 target sequence. For example, if a base atone position of an inhibitory nucleic acid is capable of hydrogenbonding with a base at the corresponding position of a miR-128 molecule,then the bases are considered to be complementary to each other at thatposition.

Although in some embodiments, 100% complementarity is desirable, it isunderstood in the art that a complementary nucleic acid sequence neednot be 100% complementary to that of its target nucleic acid to bespecifically hybridisable. A complementary nucleic acid sequence forpurposes of the present methods is specifically hybridisable whenbinding of the sequence to the target miR-128 molecule interferes withthe normal function of the target miR-128 to cause a loss of activity,and there is a sufficient degree of complementarity to avoidnon-specific binding of the sequence to non-target miR-128 sequencesunder conditions in which specific binding is desired, e.g., underphysiological conditions in the case of in vivo assays or therapeutictreatment, and in the case of in vitro assays, under conditions in whichthe assays are performed under suitable conditions of stringency. Forexample, stringent salt concentration will ordinarily be less than about750 mM NaCl and 75 mM trisodium citrate, preferably less than about 500mM NaCl and 50 mM trisodium citrate, and more preferably less than about250 mM NaCl and 25 mM trisodium citrate. Low stringency hybridizationcan be obtained in the absence of organic solvent, e.g., formamide,while high stringency hybridization can be obtained in the presence ofat least about 35% formamide, and more preferably at least about 50%formamide. Stringent temperature conditions will ordinarily includetemperatures of at least about 30° C., more preferably of at least about37° C., and most preferably of at least about 42° C. Varying additionalparameters, such as hybridization time, the concentration of detergent,e.g., sodium dodecyl sulfate (SDS), and the inclusion or exclusion ofcarrier DNA, are well known to those skilled in the art. Various levelsof stringency are accomplished by combining these various conditions asneeded. In a preferred embodiment, hybridization will occur at 30° C. in750 mM NaCl, 75 mM trisodium citrate, and 1% SDS. In a more preferredembodiment, hybridization will occur at 37° C. in 500 mM NaCl, 50 mMtrisodium citrate, 1% SDS, 35% formamide, and 100 μg/ml denatured salmonsperm DNA (ssDNA). In a most preferred embodiment, hybridization willoccur at 42° C. in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50%formamide, and 200 μg/ml ssDNA. Useful variations on these conditionswill be readily apparent to those skilled in the art.

For most applications, washing steps that follow hybridization will alsovary in stringency. Wash stringency conditions can be defined by saltconcentration and by temperature. As above, wash stringency can beincreased by decreasing salt concentration or by increasing temperature.For example, stringent salt concentration for the wash steps willpreferably be less than about 30 mM NaCl and 3 mM trisodium citrate, andmost preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate.Stringent temperature conditions for the wash steps will ordinarilyinclude a temperature of at least about 25° C., more preferably of atleast about 42° C., and even more preferably of at least about 68° C. Ina preferred embodiment, wash steps will occur at 25° C. in 30 mM NaCl, 3mM trisodium citrate, and 0.1% SDS. In a more preferred embodiment, washsteps will occur at 42° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and0.1% SDS. In a more preferred embodiment, wash steps will occur at 68°C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Additionalvariations on these conditions will be readily apparent to those skilledin the art. Hybridization techniques are well known to those skilled inthe art and are described, for example, in Benton and Davis (Science196:180, 1977); Grunstein and Hogness (Proc. Natl. Acad. Sci., USA72:3961, 1975); Ausubel et al. (Current Protocols in Molecular Biology,Wiley Interscience, New York, 2001); Berger and Kimmel (Guide toMolecular Cloning Techniques, 1987, Academic Press, New York); andSambrook et al., Molecular Cloning: A Laboratory Manual, Cold SpringHarbor Laboratory Press, New York.

In general, the inhibitory nucleic acids useful in the methods describedherein have at least 80% sequence complementarity to a target regionwithin the target nucleic acid, e.g., 90%, 95%, or 100% sequencecomplementarity to the target region within miR-128 (e.g., a targetregion comprising the seed sequence). For example, an antisense compoundin which 18 of 20 nucleobases of the antisense oligonucleotide arecomplementary, and would therefore specifically hybridize, to a targetregion would represent 90 percent complementarity. Percentcomplementarity of an inhibitory nucleic acid with a region of a targetnucleic acid can be determined routinely using basic local alignmentsearch tools (BLAST programs) (Altschul et al., J. Mol. Biol., 1990,215, 403-410; Zhang and Madden, Genome Res., 1997, 7, 649-656).Antisense and other compounds of the invention that hybridize to amiR-128 target sequence are identified through routine experimentation.In general the inhibitory nucleic acids must retain specificity fortheir target, i.e., must not directly bind to, or directly significantlyaffect expression levels of, transcripts other than the intended target.

For further disclosure regarding inhibitory nucleic acids, please seeUS2010/0317718 (antisense oligos); US2010/0249052 (double-strandedribonucleic acid (dsRNA)); US2009/0181914 and US2010/0234451 (LNAs);US2007/0191294 (siRNA analogues); US2008/0249039 (modified siRNA); andWO2010/129746 and WO2010/040112 (inhibitory nucleic acids).

Antisense

In some embodiments, the inhibitory nucleic acids are antisenseoligonucleotides. Antisense oligonucleotides are typically designed toblock expression of a DNA or RNA target by binding to the target andhalting expression at the level of transcription, translation, orsplicing. Antisense oligonucleotides of the present invention arecomplementary nucleic acid sequences designed to hybridize understringent conditions to a miR-128 target sequence. Thus,oligonucleotides are chosen that are sufficiently complementary to thetarget, i.e., that hybridize sufficiently well and with sufficientspecificity, to give the desired effect.

Modified Bases/Locked Nucleic Acids (LNAs)

In some embodiments, the inhibitory nucleic acids used in the methodsdescribed herein comprise one or more modified bonds or bases. Modifiedbases include phosphorothioate, methylphosphonate, peptide nucleicacids, or locked nucleic acid (LNA) molecules. Preferably, the modifiednucleotides are locked nucleic acid molecules, including [alpha]-L-LNAs.LNAs comprise ribonucleic acid analogues wherein the ribose ring is“locked” by a methylene bridge between the 2′-oxgygen and the4′-carbon—i.e., oligonucleotides containing at least one LNA monomer,that is, one 2′-O,4′-C-methylene-β-D-ribofuranosyl nucleotide. LNA basesform standard Watson-Crick base pairs but the locked configurationincreases the rate and stability of the basepairing reaction (Jepsen etal., Oligonucleotides, 14, 130-146 (2004)). LNAs also have increasedaffinity to base pair with RNA as compared to DNA. These propertiesrender LNAs especially useful as probes for fluorescence in situhybridization (FISH) and comparative genomic hybridization, as knockdowntools for miRNAs, and as antisense oligonucleotides to target mRNAs orother RNAs.

The LNA molecules can include molecules comprising 10-30, e.g., 12-24,e.g., 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, or 30 nucleotides in each strand, wherein one of the strands issubstantially identical, e.g., at least 80% (or more, e.g., 85%, 90%,95%, or 100%) identical, e.g., having 3, 2, 1, or 0 mismatchednucleotide(s), to a miR-128 target sequence. The LNA molecules can bechemically synthesized using methods known in the art.

The LNA molecules can be designed using any method known in the art; anumber of algorithms are known, and are commercially available (e.g., onthe interne, for example at exiqon.com). See, e.g., You et al., Nuc.Acids. Res. 34:e60 (2006); McTigue et al., Biochemistry 43:5388-405(2004); and Levin et al., Nuc. Acids. Res. 34:e142 (2006). For example,“gene walk” methods, similar to those used to design antisense oligos,can be used to optimize the inhibitory activity of the LNA (or any otherinhibitory nucleic acid described herein); for example, a series ofoligonucleotides of 10-30 nucleotides spanning the length of a targetmiR-128 sequence can be prepared, followed by testing for activity.Optionally, gaps, e.g., of 5-10 nucleotides or more, can be left betweenthe LNAs to reduce the number of oligonucleotides synthesized andtested. GC content is preferably between about 30-60%. Generalguidelines for designing LNAs are known in the art; for example, LNAsequences will bind very tightly to other LNA sequences, so it ispreferable to avoid significant complementarity within an LNA.Contiguous runs of three or more Gs or Cs, or more than four LNAresidues, should be avoided where possible (for example, it may not bepossible with very short (e.g., about 9-10 nt) oligonucleotides). Insome embodiments, the LNAs are xylo-LNAs.

For additional information regarding LNAs see U.S. Pat. Nos. 6,268,490;6,734,291; 6,770,748; 6,794,499; 7,034,133; 7,053,207; 7,060,809;7,084,125; and 7,572,582; and U.S. Pre-Grant Pub. Nos. 20100267018;20100261175; and 20100035968; Koshkin et al. Tetrahedron 54, 3607-3630(1998); Obika et al. Tetrahedron Lett. 39, 5401-5404 (1998); Jepsen etal., Oligonucleotides 14:130-146 (2004); Kauppinen et al., Drug Disc.Today 2(3):287-290 (2005); and Ponting et al., Cell 136(4):629-641(2009), and references cited therein.

In some embodiments of the methods described herein, the inhibitorynucleic acid is or comprises TTCACTGTG (SEQ ID NO:10) or GGTTCACTGTG(SEQ ID NO:11), wherein all or some of the nucleic acids are locked andthe backbone is a phosphorothioate backbone (e.g., all locked in SEQ IDNO:9 and some (e.g., at least 50%) locked in SEQ ID NO:10). In someembodiments of the methods described herein, the inhibitory nucleic acidis or comprises SEQ ID NO:8.

Antagomirs

In some embodiments, the antisense is an antagomir. Antagomirs arechemically modified antisense oligonucleotides that target a miR-128target sequence. For example, an antagomir for use in the methodsdescribed herein can include a nucleotide sequence sufficientlycomplementary to hybridize to a miR-128 target sequence of about 12 to25 nucleotides, preferably about 15 to 23 nucleotides.

In general, antagomirs include a cholesterol moiety, e.g., at the3′-end. In some embodiments, antagomirs have various modifications forRNase protection and pharmacologic properties such as enhanced tissueand cellular uptake. For example, In addition to the modificationsdiscussed above for antisense oligos, an antagomir can have one or moreof complete or partial 2′-O-methylation of sugar and/or aphosphorothioate backbone. Phosphorothioate modifications provideprotection against RNase activity and their lipophilicity contributes toenhanced tissue uptake. In some embodiments, the antagomir can includesix phosphorothioate backbone modifications; two phosphorothioates arelocated at the 5′-end and four at the 3′-end. See, e.g., Krutzfeldt etal., Nature 438, 685-689 (2005); Czech, N Engl J Med 2006; 354:1194-1195(2006); Robertson et al., Silence. 1:10 (2010); Marquez and McCaffrey,Hum Gene Ther. 19(1):27-38 (2008); van Rooij et al., Circ Res.103(9):919-928 (2008); and Liu et al., Int. J. Mol. Sci. 9:978-999(2008). Antagomirs useful in the present methods can also be modifiedwith respect to their length or otherwise the number of nucleotidesmaking up the antagomir. The antagomirs must retain specificity fortheir target, i.e., must not directly bind to, or directly significantlyaffect expression levels of, transcripts other than the intended target.

In some embodiments, the inhibitory nucleic acid is locked and includesa cholesterol moiety (e.g., a locked antagomir).

Making and Using Inhibitory Nucleic Acids

The nucleic acid sequences used to practice the methods describedherein, whether RNA, cDNA, genomic DNA, vectors, viruses or hybridsthereof, can be isolated from a variety of sources, geneticallyengineered, amplified, and/or expressed/generated recombinantly.Recombinant nucleic acid sequences can be individually isolated orcloned and tested for a desired activity. Any recombinant expressionsystem can be used, including e.g. in vitro, bacterial, fungal,mammalian, yeast, insect or plant cell expression systems.

Nucleic acid sequences of the invention can be inserted into deliveryvectors and expressed from transcription units within the vectors. Therecombinant vectors can be DNA plasmids or viral vectors. Generation ofthe vector construct can be accomplished using any suitable geneticengineering techniques well known in the art, including, withoutlimitation, the standard techniques of PCR, oligonucleotide synthesis,restriction endonuclease digestion, ligation, transformation, plasmidpurification, and DNA sequencing, for example as described in Sambrooket al. Molecular Cloning: A Laboratory Manual. (1989)), Coffin et al.(Retroviruses. (1997)) and “RNA Viruses: A Practical Approach” (Alan J.Cann, Ed., Oxford University Press, (2000)). As will be apparent to oneof ordinary skill in the art, a variety of suitable vectors areavailable for transferring nucleic acids of the invention into cells.The selection of an appropriate vector to deliver nucleic acids andoptimization of the conditions for insertion of the selected expressionvector into the cell, are within the scope of one of ordinary skill inthe art without the need for undue experimentation. Viral vectorscomprise a nucleotide sequence having sequences for the production ofrecombinant virus in a packaging cell. Viral vectors expressing nucleicacids of the invention can be constructed based on viral backbonesincluding, but not limited to, a retrovirus, lentivirus, adenovirus,adeno-associated virus, pox virus or alphavirus. The recombinant vectorscapable of expressing the nucleic acids of the invention can bedelivered as described herein, and persist in target cells (e.g., stabletransformants).

Nucleic acid sequences used to practice this invention can besynthesized in vitro by well-known chemical synthesis techniques, asdescribed in, e.g., Adams (1983) J. Am. Chem. Soc. 105:661; Belousov(1997) Nucleic Acids Res. 25:3440-3444; Frenkel (1995) Free Radic. Biol.Med. 19:373-380; Blommers (1994) Biochemistry 33:7886-7896; Narang(1979) Meth. Enzymol. 68:90; Brown (1979) Meth. Enzymol. 68:109;Beaucage (1981) Tetra. Lett. 22:1859; U.S. Pat. No. 4,458,066.

Nucleic acid sequences of the invention can be stabilized againstnucleolytic degradation such as by the incorporation of a modification,e.g., a nucleotide modification. For example, nucleic acid sequences ofthe invention includes a phosphorothioate at least the first, second, orthird internucleotide linkage at the 5′ or 3′ end of the nucleotidesequence. As another example, the nucleic acid sequence can include a2′-modified nucleotide, e.g., a 2′-deoxy, 2′-deoxy-2′-fluoro,2′-O-methyl, 2′-O-methoxyethyl (2′-O-MOE), 2′-O-aminopropyl (2′-O-AP),2′-O-dimethylaminoethyl (2′-O-DMAOE), 2′-O-dimethylaminopropyl(2′-O-DMAP), 2′-O-dimethylaminoethyloxyethyl (2′-O-DMAEOE), or2′-O—N-methylacetamido (2′-O-NMA). As another example, the nucleic acidsequence can include at least one 2′-O-methyl-modified nucleotide, andin some embodiments, all of the nucleotides include a 2′-O-methylmodification. In some embodiments, the nucleic acids are “locked,” i.e.,comprise nucleic acid analogues in which the ribose ring is “locked” bya methylene bridge connecting the 2′-O atom and the 4′-C atom (see,e.g., Kaupinnen et al., Drug Disc. Today 2(3):287-290 (2005); Koshkin etal., J. Am. Chem. Soc., 120(50):13252-13253 (1998)). For additionalmodifications see US 20100004320, US 20090298916, and US 20090143326.

Techniques for the manipulation of nucleic acids used to practice thisinvention, such as, e.g., subcloning, labeling probes (e.g.,random-primer labeling using Klenow polymerase, nick translation,amplification), sequencing, hybridization and the like are welldescribed in the scientific and patent literature, see, e.g., Sambrooket al., Molecular Cloning; A Laboratory Manual 3d ed. (2001); CurrentProtocols in Molecular Biology, Ausubel et al., eds. (John Wiley & Sons,Inc., New York 2010); Kriegler, Gene Transfer and Expression: ALaboratory Manual (1990); Laboratory Techniques In Biochemistry AndMolecular Biology: Hybridization With Nucleic Acid Probes, Part I.Theory and Nucleic Acid Preparation, Tijssen, ed. Elsevier, N.Y. (1993).

Pharmaceutical Compositions

The methods described herein can include the administration ofpharmaceutical compositions and formulations comprising inhibitorynucleic acid sequences designed to target miR-128.

In some embodiments, the compositions are formulated with apharmaceutically acceptable carrier. The pharmaceutical compositions andformulations can be administered parenterally, topically, orally or bylocal administration, such as by aerosol or transdermally. Thepharmaceutical compositions can be formulated in any way and can beadministered in a variety of unit dosage forms depending upon thecondition or disease and the degree of illness, the general medicalcondition of each patient, the resulting preferred method ofadministration and the like. Details on techniques for formulation andadministration of pharmaceuticals are well described in the scientificand patent literature, see, e.g., Remington: The Science and Practice ofPharmacy, 21st ed., 2005.

The inhibitory nucleic acids can be administered alone or as a componentof a pharmaceutical formulation (composition). The compounds may beformulated for administration, in any convenient way for use in human orveterinary medicine. Wetting agents, emulsifiers and lubricants, such assodium lauryl sulfate and magnesium stearate, as well as coloringagents, release agents, coating agents, sweetening, flavoring andperfuming agents, preservatives and antioxidants can also be present inthe compositions.

Formulations of the compositions of the invention include those suitablefor parenteral administration. The formulations may conveniently bepresented in unit dosage form and may be prepared by any methods wellknown in the art of pharmacy. The amount of active ingredient (e.g.,nucleic acid sequences of this invention) which can be combined with acarrier material to produce a single dosage form can vary depending uponthe host being treated, the particular mode of administration. Theamount of active ingredient which can be combined with a carriermaterial to produce a single dosage form will generally be that amountof the compound which produces a therapeutic effect, e.g., reduction inmiR-128 levels and/or reduction in a symptom of DMD, BMD, or DCM.

Pharmaceutical formulations of this invention can be prepared accordingto any method known to the art for the manufacture of pharmaceuticals.Such drugs can contain, for example, preserving agents. A formulationcan be admixtured with nontoxic pharmaceutically acceptable excipientswhich are suitable for manufacture. Formulations may comprise one ormore diluents, emulsifiers, preservatives, buffers, excipients, etc. andmay be provided in such forms as liquids, powders, emulsions,lyophilized powders, controlled release formulations, on patches, inimplants, etc.

Aqueous suspensions can contain an active agent (e.g., nucleic acidsequences of the invention) in admixture with excipients suitable forthe manufacture of aqueous suspensions, e.g., for aqueous intradermalinjections. Such excipients include a suspending agent, such as sodiumcarboxymethylcellulose, methylcellulose, hydroxypropylmethylcellulose,sodium alginate, polyvinylpyrrolidone, gum tragacanth and gum acacia,and dispersing or wetting agents such as a naturally occurringphosphatide (e.g., lecithin), a condensation product of an alkyleneoxide with a fatty acid (e.g., polyoxyethylene stearate), a condensationproduct of ethylene oxide with a long chain aliphatic alcohol (e.g.,heptadecaethylene oxycetanol), a condensation product of ethylene oxidewith a partial ester derived from a fatty acid and a hexitol (e.g.,polyoxyethylene sorbitol mono-oleate), or a condensation product ofethylene oxide with a partial ester derived from fatty acid and ahexitol anhydride (e.g., polyoxyethylene sorbitan mono-oleate). Theaqueous suspension can also contain one or more preservatives such asethyl or n-propyl p-hydroxybenzoate, one or more coloring agents, one ormore flavoring agents and one or more sweetening agents, such assucrose, aspartame or saccharin. Formulations can be adjusted forosmolarity.

In some embodiments, oil-based pharmaceuticals are used foradministration of nucleic acid sequences as described herein. As anexample of an injectable oil vehicle, see Minto (1997) J. Pharmacol.Exp. Ther. 281:93-102.

Pharmaceutical formulations can also be in the form of oil-in-wateremulsions. The oily phase can be a vegetable oil or a mineral oil,described above, or a mixture of these. Suitable emulsifying agentsinclude naturally-occurring gums, such as gum acacia and gum tragacanth,naturally occurring phosphatides, such as soybean lecithin, esters orpartial esters derived from fatty acids and hexitol anhydrides, such assorbitan mono-oleate, and condensation products of these partial esterswith ethylene oxide, such as polyoxyethylene sorbitan mono-oleate. Theemulsion can also contain sweetening agents and flavoring agents, as inthe formulation of syrups and elixirs. Such formulations can alsocontain a demulcent, a preservative, or a coloring agent. In alternativeembodiments, these injectable oil-in-water emulsions of the inventioncomprise a paraffin oil, a sorbitan monooleate, an ethoxylated sorbitanmonooleate and/or an ethoxylated sorbitan trioleate.

In some embodiments, the pharmaceutical compounds can also be deliveredas microspheres for slow release in the body. For example, microspherescan be administered via intradermal injection of drug which slowlyrelease subcutaneously; see Rao (1995) J. Biomater Sci. Polym. Ed.7:623-645; as biodegradable and injectable gel formulations, see, e.g.,Gao (1995) Pharm. Res. 12:857-863 (1995); or, as microspheres for oraladministration, see, e.g., Eyles (1997) J. Pharm. Pharmacol. 49:669-674.

In some embodiments, the pharmaceutical compounds can be parenterallyadministered, such as by intravenous (IV) administration oradministration into a body cavity or lumen of an organ. Theseformulations can comprise a solution of active agent dissolved in apharmaceutically acceptable carrier. Acceptable vehicles and solventsthat can be employed are water and Ringer's solution, an isotonic sodiumchloride. In addition, sterile fixed oils can be employed as a solventor suspending medium. For this purpose any bland fixed oil can beemployed including synthetic mono- or diglycerides. In addition, fattyacids such as oleic acid can likewise be used in the preparation ofinjectables. These solutions are sterile and generally free ofundesirable matter. These formulations may be sterilized byconventional, well known sterilization techniques. The formulations maycontain pharmaceutically acceptable auxiliary substances as required toapproximate physiological conditions such as pH adjusting and bufferingagents, toxicity adjusting agents, e.g., sodium acetate, sodiumchloride, potassium chloride, calcium chloride, sodium lactate and thelike. The concentration of active agent in these formulations can varywidely, and will be selected primarily based on fluid volumes,viscosities, body weight, and the like, in accordance with theparticular mode of administration selected and the patient's needs. ForIV administration, the formulation can be a sterile injectablepreparation, such as a sterile injectable aqueous or oleaginoussuspension. This suspension can be formulated using those suitabledispersing or wetting agents and suspending agents. The sterileinjectable preparation can also be a suspension in a nontoxicparenterally-acceptable diluent or solvent, such as a solution of1,3-butanediol. The administration can be by bolus or continuousinfusion (e.g., substantially uninterrupted introduction into a bloodvessel for a specified period of time).

In some embodiments, the pharmaceutical compounds and formulations canbe lyophilized. Stable lyophilized formulations comprising an inhibitorynucleic acid can be made by lyophilizing a solution comprising apharmaceutical of the invention and a bulking agent, e.g., mannitol,trehalose, raffinose, and sucrose or mixtures thereof. A process forpreparing a stable lyophilized formulation can include lyophilizing asolution about 2.5 mg/mL protein, about 15 mg/mL sucrose, about 19 mg/mLNaCl, and a sodium citrate buffer having a pH greater than 5.5 but lessthan 6.5. See, e.g., U.S. 20040028670.

The compositions and formulations can be delivered by the use ofliposomes. By using liposomes, particularly where the liposome surfacecarries ligands specific for target cells, or are otherwisepreferentially directed to a specific organ, one can focus the deliveryof the active agent into target cells in vivo. See, e.g., U.S. Pat. Nos.6,063,400; 6,007,839; Al-Muhammed (1996) J. Microencapsul. 13:293-306;Chonn (1995) Curr. Opin. Biotechnol. 6:698-708; Ostro (1989) Am. J.Hosp. Pharm. 46:1576-1587. As used in the present invention, the term“liposome” means a vesicle composed of amphiphilic lipids arranged in abilayer or bilayers. Liposomes are unilamellar or multilamellar vesiclesthat have a membrane formed from a lipophilic material and an aqueousinterior that contains the composition to be delivered. Cationicliposomes are positively charged liposomes that are believed to interactwith negatively charged DNA molecules to form a stable complex.Liposomes that are pH-sensitive or negatively-charged are believed toentrap DNA rather than complex with it. Both cationic and noncationicliposomes have been used to deliver DNA to cells.

Liposomes can also include “sterically stabilized” liposomes, i.e.,liposomes comprising one or more specialized lipids. When incorporatedinto liposomes, these specialized lipids result in liposomes withenhanced circulation lifetimes relative to liposomes lacking suchspecialized lipids. Examples of sterically stabilized liposomes arethose in which part of the vesicle-forming lipid portion of the liposomecomprises one or more glycolipids or is derivatized with one or morehydrophilic polymers, such as a polyethylene glycol (PEG) moiety.Liposomes and their uses are further described in U.S. Pat. No.6,287,860.

The formulations of the invention can be administered for prophylacticand/or therapeutic treatments. In some embodiments, for therapeuticapplications, compositions are administered to a subject who is need ofreduced triglyceride levels, or who is at risk of or has a disorderdescribed herein, in an amount sufficient to cure, alleviate orpartially arrest the clinical manifestations of the disorder or itscomplications; this can be called a therapeutically effective amount.For example, in some embodiments, pharmaceutical compositions of theinvention are administered in an amount sufficient to decrease serumlevels of triglycerides in the subject.

The amount of pharmaceutical composition adequate to accomplish this isa therapeutically effective dose. The dosage schedule and amountseffective for this use, i.e., the dosing regimen, will depend upon avariety of factors, including the stage of the disease or condition, theseverity of the disease or condition, the general state of the patient'shealth, the patient's physical status, age and the like. In calculatingthe dosage regimen for a patient, the mode of administration also istaken into consideration.

The dosage regimen also takes into consideration pharmacokineticsparameters well known in the art, i.e., the active agents' rate ofabsorption, bioavailability, metabolism, clearance, and the like (see,e.g., Hidalgo-Aragones (1996) J. Steroid Biochem. Mol. Biol. 58:611-617;Groning (1996) Pharmazie 51:337-341; Fotherby (1996) Contraception54:59-69; Johnson (1995) J. Pharm. Sci. 84:1144-1146; Rohatagi (1995)Pharmazie 50:610-613; Brophy (1983) Eur. J. Clin. Pharmacol. 24:103-108;Remington: The Science and Practice of Pharmacy, 21st ed., 2005). Thestate of the art allows the clinician to determine the dosage regimenfor each individual patient, active agent and disease or conditiontreated. Guidelines provided for similar compositions used aspharmaceuticals can be used as guidance to determine the dosageregiment, i.e., dose schedule and dosage levels, administered practicingthe methods of the invention are correct and appropriate.

Single or multiple administrations of formulations can be givendepending on for example: the dosage and frequency as required andtolerated by the patient, the degree and amount of therapeutic effectgenerated after each administration (e.g., effect on tumor size orgrowth), and the like. The formulations should provide a sufficientquantity of active agent to effectively treat, prevent or ameliorateconditions, diseases or symptoms.

The specificity, stability and safety of ASO technologies have improveddramatically over the last 5-10 years⁶⁷. Various studies have reportedsuccessful mammalian dosing using complementary nucleic acid sequences.For example, Esau C., et al., (2006) Cell Metabolism, 3(2):87-98reported dosing of normal mice with intraperitoneal doses of miR-122antisense oligonucleotide ranging from 12.5 to 75 mg/kg twice weekly for4 weeks. The mice appeared healthy and normal at the end of treatment,with no loss of body weight or reduced food intake. Plasma transaminaselevels were in the normal range (AST ¾ 45, ALT ¾ 35) for all doses withthe exception of the 75 mg/kg dose of miR-122 ASO, which showed a verymild increase in ALT and AST levels. They concluded that 50 mg/kg was aneffective, non-toxic dose. Another study by Kriitzfeldt J., et al.,(2005) Nature 438, 685-689, injected antagomirs to silence miR-122 inmice using a total dose of 80, 160 or 240 mg per kg body weight. Thehighest dose resulted in a complete loss of miR-122 signal. In yetanother study, locked nucleic acids (“LNAs”) were successfully appliedin primates to silence miR-122. Elmen J., et al., (2008) Nature 452,896-899, report that efficient silencing of miR-122 was achieved inprimates by three doses of 10 mg kg-1 LNA-anti-miR, leading to along-lasting and reversible decrease in total plasma cholesterol withoutany evidence for LNA-associated toxicities or histopathological changesin the study animals.

In preferred embodiments, Locked Nucleic Acid (LNA) ASO technology isused to target miR-128 in DMD. The LNA chemistry affords stronglyincreased target affinity and specificity, and is combined with aphosphorothioate backbone of the ASO for increased in vivo stability andpharmacokinetics⁶⁸. This ASO chemistry also compares favorably witholder technologies such as morpholino-based chemistries. Terminal LNAASO half-life in circulation is typically 2-3 weeks in mammals, based onmultiple studies in mice and non-human primates with an LNA ASOtargeting miR-33 (e.g., Rottiers et al. Science Transl. Med. 2013⁶¹),with LNAASOs detected in tissues up to 7 weeks after a single injection.This allows once-weekly subcutaneous injection in mice, and possiblyonce-monthly subcutaneous dosing in humans due to decreased kidneyclearance of LNAASOs in humans as compared with rodents. In miR-128-1LNA ASO studies with once-weekly subcutaneous delivery at 2.5-10 mg/kgin several mouse models of cardiometabolic disease (obesity, Type 2diabetes, NAFLD/NASH, atherosclerosis), strong target engagement wasobserved in all major metabolic tissues, including skeletal muscle,liver, subcutaneous and visceral WAT, and BAT, with profound beneficialeffects on whole animal metabolism (Wagschal et al. Nature Med. 2015⁶²and unpublished data). Additionally, no significant elevation of liverand kidney toxicity parameters was observed, suggesting thatanti-miR-128-1 LNA ASO treatment is well tolerated, at least in mice. Insome embodiments, the methods include the administration of 1-10 mg/kg,2-5 mg/kg, about 1×/month, 2×/month, or 1×/week.

In some embodiments, the methods described herein can includeco-administration with other drugs or pharmaceuticals, e.g.,compositions for treating DMD. For example, the inhibitory nucleic acidscan be co-administered with drugs for treating or reducing risk of adisorder described herein. For example, exon-skipping antisenseoligonucleotides (ASOs) that correct missplicing can be used, e.g., asdescribed in Siva et al., Nucleic Acid Ther. 2014 Feb. 1; 24(1): 69-86;Scotti and Swanson, Nature Reviews Genetics 17:19-32 (2016). Forexample, bicyclic-locked nucleic acids (LNAs), ethylene-bridged nucleicacids (ENAs), 2′-O-methyl phosphorothioate AO (2OME-PSs), peptidenucleic acids (PNAs), or phosphorodiamidate morpholino oligomers (PMOs)have been described that correct missplicing in clinical trials andanimal models; see, e.g., Brolin and Shiraishi, Artif DNA PNA XNA. 2011January-March; 2(1): 6-15; Scotti and Swanson, Nature Reviews Genetics17:19-32 (2016); Touznik et al., Expert Opin Biol Ther. 2014 June;14(6):809-19. The ASOs can be delivered, e.g., parenterally in liposomalcomplexes, e.g., cationic lipoplexes, or using a viral vector, e.g., alentivirus, adenovirus, or adeno-associated virus. See e.g., Jarver etal., Nucleic Acid Ther. 2014; 24(1):37-47; Aartsma-Rus et al., Hum GeneTher. 2014; 25(10):885-892, McNally and Wyatt, J Clin Invest. 2016 Apr.1; 126(4):1236-8; Imbert et al., Genes 2017, 8(2), 51;doi:10.3390/genes8020051. Specific ASOs for use in exon 51 skippingtherapy, e.g., in DMD, include PRO051 (2OME-PS, Netherlands) andAVI-4658 (PMO, UK). A plurality of ASOs can also be used, e.g., toinduce exon skipping in multiple exons; see, e.g., Wood et al., Brain.2010 April; 133(Pt 4): 957-72 See also Fletcher et al., Mol Ther NucleicAcids. 2012 October; 1(10): e48; McClorey et al., Curr Opin Pharmacol.2005 October; 5(5):529-34. Small molecule therapeutics can also be used,e.g., PTC124, a 284.24-Da, achiral, 1,2,4-oxadiazole linked tofluorobenzene and benzoic acid rings, which selectively inducesribosomal read-through of premature but not normal termination codons,see Welch et al., Nature 447: 87-91, 2007, and has been used in clinicaltrials for DMD.

EXAMPLES

The invention is further described in the following examples, which donot limit the scope of the invention described in the claims.

Example 1. The miR-128-1 microRNA is a Potential Disease Modifier andTherapeutic Target in DMD

While essentially all disease treatments to date have focused ontargeting functions or activity of genes and proteins, regulatorynon-coding RNAs such as microRNAs (miRNAs) have recently come to thefore as potential modifiers and therapeutic targets in a range ofdiseases, including DMD. It was hypothesized that the miR-128-1 miRNAmight represent an intriguing therapeutic target in DMD due to itsregulation of skeletal muscle metabolism and direct targeting of severalkey modifiers downstream of dystrophin loss.

Relevant to this proposal and as alluded to above, we identifiedmiR-128-1 as implicated in regulating a number of the genes shown to actas modifiers of DMD phenotypes, including PGC-1α, AMPKα2, SIRT1, JAG1and Wnt7A, as well as other metabolic regulators such as PPARα, PPARγ,ULK1, CPT1β, and others. During studies of the effects of LNA ASOstargeting miR-128-1 in diet-induced obese mice (once-weekly tail-veininjection of 10 mg/kg of a 9mer all LNA ASO (SEQ ID NO:9) directedagainst the seed sequence of miR-128, for 16 weeks into high-fat (60%fat) diet-fed male C57BL/6J mice starting at 6 weeks of age), weobserved marked beneficial energy metabolism-related effects in skeletalmuscle, including increased mitochondrial numbers and elevatedexpression of energy expenditure genes such as PGC-1α, AMPKα2, CPT1β,and PPARα, several of which have been implicated as downstream modifiersof DMD pathologies as discussed above (FIGS. 1A-C).

Consistent with our findings of miR-128-1 as a central regulator ofmetabolic homeostasis in skeletal muscle, and with verified andpredicted targets implicated as key modifiers of the etiology of DMD,members of our team (Kunkel et al.) have independently identifiedmiR-128-1 as an important regulator of proliferation and differentiationin muscle side population (SP) cells', a cell type considered torepresent muscle stem cells with high mesenchymal potential, and apossible muscular dystrophy therapy. They found in this study thatexpression of miR-128-1 is elevated in SP cells, but decreases duringcontinued culture in vitro. Furthermore, over-expression of miR-128-1inhibited SP cell proliferation and differentiation potential. Thesefindings suggest that miR-128-1 contributes to the maintenance of thequiescent state of SP cells, and may act to prevent their regenerativedifferentiation potential.

Over-expression and antisense targeting of miR-128-1 in differentiatedmouse C2C12 myotubes results in altered expression of a number ofpredicted targets involved in controlling mitochondrial biogenesis andregulation of energy expenditure (FIGS. 8A-C).

Example 2. Evaluation of Downstream Effects of Mir-128-1 Over-expressionand Antisense Inhibition in Skeletal Muscle Cells

As discussed above, abnormal mitochondrial function and defectiveautophagy/mitophagy has been implicated in DMD, and several rescuestrategies such as PGC-1α over-expression, as well as AMPK and SIRT1activation by metformin and resveratrol/nicotinamide riboside,respectively, act to promote mitochondrial health and numbers, as wellas stimulating autophagy/mitophagy.

We have shown that antisense-mediated inhibition of miR-128-1 indiet-induced obese (DIO) mice results in an increase in skeletal musclemitochondrial number, and elevated expression of several direct andindirect miR-128-1 regulated genes involved in mitochondrial biology andenergy homeostasis (FIGS. 6A-C).

It was hypothesized that anti-miR-128-1 treatment might cooperate withagents that stimulate AMPK and SIRT1, such as AICAR/metformin andresveratrol/nicotinamide riboside, respectively. To determine the impactof anti-miR-128-1 treatment alone and in combination with these AMPK andsirtuin activators on metabolic health of muscle cell from normalindividuals and DMD patients, we queried effects on muscle cellphysiology, including AICAR-dependent increase in energy expenditureregulators, including AMPKa2, PGC-1α, PPARα, and CPT1β, as well asmitochondrial number (determined by levels of mitochondrial markersCOXI-III) and morphology (visualized with MitoTracker Green), Seahorsestudies of mitochondrial respiration as a read-out of mitochondrialhealth and bioenergetics output capacity, and autophagy (as judged bystaining cells with the LC3 autophagy marker). We also determined theeffects of miR-128-1 manipulations on additional metabolic parameters inmuscle cells, such as fatty acid eta-oxidation as a read-out ofmitochondrial activity. As a proof-of-principle study we haveinvestigated the effect of anti-miR-128-1 treatment of C2C12 myoblasts,and indeed found potentiation of AICAR stimulation of energy regulators,elevated mitochondrial respiration, and increased fatty acideta-oxidation upon miR-128-1 knock-down (FIGS. 8A-F), providing strongsupport for the success of the proposed studies.

Example 3. miR-128-1 Antisense Inhibition can Prevent Muscle DiseaseProgression in Dystrophin-Deficient Zebrafish

We performed a short-term study with the sapje-like zebrafish DMD modelusing candidate LNA ASOs. 100-200 embryos from mating pairs ofheterozygous sapje-like mutant fish were injected with microneedle atthe one cell stage on 0 dpf at 50 fmol dosage of anti-miR128-1 9mer orcontrol LNA ASOs. The experiment was independently repeated three times.All plates containing embryos were incubated at 28° C. At 4 dpf, thebirefringence of all fish were assessed using a dissecting microscopeand examined for black spots in the dorsal muscles (indicator of musclemyofiber weakness and myofiber disorganization) as shown in FIG. 9A.Since the muscle phenotype in these mutant fish is transmitted in arecessive manner, ˜25% of the control offspring will exhibit the musclebirefringence phenotype. Our initial study showed that the 9mer-LNA ASOat 50 fmol consistently reduced the percentage of affected birefringencefish in sapje-like fish to 14% (FIG. 9B), and gene sequencing from thelast experiment confirmed that >30% of dystrophin −/− fish exhibitednormal muscle structure (FIG. 9C). In the initial screening DanioVisiontracking system was used to monitor single zebrafish larvae movement in24-well plates. At 5 dpf Sapje-like fish after injection were monitoredindividually in a 24-well plate at 28° C. in the system for 20 minsafter acclimation. Fish movement was tracked and mapped, and analyzedfor swimming velocity and distance travelled.

The results showed that the 9mer-LNA ASO significantly increaseddystrophin−/− sapje-like fish activity to a level comparable to wildtype zebrafish level (FIG. 10A-B). Taken together, these resultsdemonstrate that there is efficacy of miR-128 inhibition indystrophin−/− zebrafish and that we can optimize the dosage andtreatment conditions to be able to distinguish between effective andnon-effective treatments on the muscle phenotype in the zebrafish modelof DMD.

Example 4. Anti-miR-128-1 LNA ASO Treatment of mdx Mice

Additional Experiments Included Treatment with Potent and HighlySpecific LNA ASOs Targeting miR-128-1 and Control Scrambled LNA ASO inmdx Male Mice Age-matched mice were injected subcutaneously with 10mg/kg of LNA ASO (SEQ ID NO:8) in saline or scrambled control LNA ASOonce-weekly starting at six weeks of age. Treatment continued for 10weeks, with motor function assessment every two weeks during treatment,including by grip test and molecular analyses. As shown in FIG. 11A,anti-miR-128-1 treatment resulted in significant target engagement inskeletal muscle (TA), decreasing miR-128-1 levels significantly by ˜50%.Consistent with miR-128-1 contributing to deleterious phenotypes in thisDMD model, we observed a marked decrease in circulating creatine kinase(correlating with muscle damage and a hallmark of DMD) (FIG. 11B), aswell as improvement in grip strength (FIG. 11C). These encouragingresults support the use of anti-miR-128 LNA ASOs in DMD.

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OTHER EMBODIMENTS

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

What is claimed is:
 1. A method of treating a subject who has Duchennemuscular dystrophy (DMD) or Becker muscular dystrophy (BMD), the methodcomprising administering to the subject: (i) a therapeutically effectiveamount of an inhibitory nucleic acid that is complementary to all orpart of any of SEQ ID NOs: 1-6, and (ii) an additional treatment for DMDor BMD.
 2. The method of claim 1, wherein the method increases musclemass, or reduces or delays muscle loss, in the subject.
 3. The method ofclaim 1, wherein the method treats or reduces risk of developing dilatedcardiomyopathy (DCM) in the subject.
 4. The method of claim 1, whereinthe inhibitory nucleic acid is complementary to all or part of SEQ IDNO:2.
 5. The method of claim 1, wherein the inhibitory nucleic acid iscomplementary to at least nucleotides 2-7 (5′-CACAGU-3′) of SEQ ID NO:3.6. The method of claim 1, wherein the inhibitory nucleic acid is anantisense oligonucleotide.
 7. The method of claim 6, wherein theantisense oligonucleotide comprises a sequence that is complementary toSEQ ID NO:3.
 8. The method of claim 6, wherein the antisenseoligonucleotide is an antagomir.
 9. The method of claim 1, wherein theinhibitory nucleic acid is an interfering RNA.
 10. The method of claim9, wherein the interfering RNA is a small hairpin RNA (shRNA) or smallinterfering RNA (siRNA).
 11. The method of claim 1, wherein theinhibitory nucleic acid sequence inhibits post-transcriptionalprocessing of SEQ ID NO:1 or
 5. 12. The method of claim 1, wherein thesubject has DMD.
 13. The method of claim 12, further comprisingselecting a subject on the basis that they have DMD.
 14. The method ofclaim 1, wherein the inhibitory nucleic acid has at least one lockednucleotide.
 15. The method of claim 1, wherein the inhibitory nucleicacid has a phosphorothioate backbone.
 16. The method of claim 1, whereinthe inhibitory nucleic acid is or comprises TTCACTGTG (SEQ ID NO:10) orGGTTCACTGTG (SEQ ID NO:11).
 17. The method of claim 16, wherein at leasthalf of the nucleic acids are locked.
 18. The method of claim 16,wherein all of the nucleic acids are locked.
 19. The method of claim 16,wherein the backbone is a phosphorothioate backbone.
 20. The method ofclaim 1, wherein the inhibitory nucleic acid is or comprises+G*+G*+T*+T*C*A*C*+T*+G*+T*+G (SEQ ID NO:8).
 21. The method of claim 20,wherein the inhibitory nucleic acid is administered at a dose of 1-20mg/kg.
 22. The method of claim 21, wherein the inhibitory nucleic acidis administered once or twice per month.
 23. The method of claim 1,wherein the additional treatment for DMD or BMD is an exon-skippingantisense oligonucleotide (ASO).
 24. The method of claim 23, wherein theexon-skipping ASO is PRO051 or AVI-4658.
 25. The method of claim 1,wherein the additional treatment for DMD or BMD is PTC124, metformin,resveratrol, or nicotinamide riboside.
 26. A pharmaceutical compositioncomprising an inhibitory nucleic acid that is complementary to all orpart of any of SEQ ID NOs: 1-6, optionally which is or comprises+G*+G*+T*+T*C*A*C*+T*+G*+T*+G (SEQ ID NO:8), and an additionaltherapeutic for DMD or BMD.
 27. The pharmaceutical composition of claim26, wherein the additional treatment for DMD or BMD is an exon-skippingantisense oligonucleotide (ASO).
 28. The pharmaceutical composition ofclaim 27, wherein the exon-skipping ASO is PRO051 or AVI-4658.
 29. Thepharmaceutical composition of claim 26, wherein the additional treatmentfor DMD or BMD is PTC124, metformin, resveratrol, or nicotinamideriboside.